I thought you needed 130+ karma to pick the choice where your Aradia joins the original, not to pick the choice where you fight her. On top of that, you can gain... 165, karma, I think? So I believe you can achieve this without doing Suzune's side-plot. Or at least, you don't need to complete the entire plot and you'll still gain enough karma for the choice.
As a side note, the choice at the end after you fight the original Aradia does absolutely fuck all. No matter what you choose, the same thing happen. The only choice that matters is the one before the fight itself... I don't know if this is intended or not. It may or may not be a bug.
As for the whole message about the cycle of revenge...
Unfortunately, it's undermined pretty heavily by how the world and story is structured.
The majority of the members of this fictional church are all insane and all of them seem to end up as rapists at some point or another. If I'm not mistaken, several of the journals show that, and they show that they victimize people that have nothing to do with anything (like that girl that ended up being used as a test for the tentacles, or the other girl used as a test for that pleasure torture chair thing). They cooperate with the farm too as far as I can tell.
Quite frankly, that nutso organization NEEDS to be stopped, and you're not gonna get that done with pretty words and idealism.
On top of that, Suzune is a poor example of the negatives of the cycle of revenge. To begin with, her insane brother needed to be stopped too. Then there's the fact that the cycle of revenge generally involves the consequences of completed revenge, not just pursuing it, and that's never shown in game. There's never an example of say, a friend or family member of a the revenge victim being affected negatively. The closest you get, I think, are the maids? Didn't they admire Candore or something and were shocked when they heard that she was defeated and raped?
Either way, anyone wanting to take revenge for rapist murderers (and make no mistake, most of the victims of both Aradia and the original Aradia are both of these things) has some MAJOR screws loose. Realistically, those sorts of people are assholes to everyone around them, especially their own family, so it's unlikely that there'd be anyone worth a damn that would want to take revenge for the majority of them.
So yeah...
There's some issues with the story. XD
But hey. The hentai is still 120% top notch.